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You say that you are moving your saddle both towards and away, but even the smallest increments of towards and away will make a difference. Therefore, don't start playing with the truss rod. Just be sure, if you aren't already doing so, to try very small increments of adjustment, likening it to the fine tuners on violins.
All of that being said, do know, too, that, every once in a while, a new strings will be imperfect. For example, a tech I know says that that is why he doesn't like to use DR strings: occasionally, he will come across a string that just will not intonate.
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